9DDB | pdb_00009ddb

Deposited: 2024-08-27 Released: 2025-09-10
Deposition Author(s): Roark, R.S., Shapiro, L., Kwong, P.D.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Macromolecule Content

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoprotein B	A [auth C], B [auth D], C [auth E]	808	Human alphaherpesvirus 1	Mutation(s): 2 Gene Names: UL27, HHV1gp041
UniProt
Find proteins for A1Z0P7 (Human herpesvirus 1) Explore A1Z0P7 Go to UniProtKB: A1Z0P7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A1Z0P7
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A [auth C] Focus chain B [auth D] Focus chain C [auth E]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth A], F, H	2		N-Glycosylation	Interactions Focus chain D [auth A] Focus chain F Focus chain H Interactions & Density Focus chain D [auth A] Focus chain F Focus chain H
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth B], G, I	3		N-Glycosylation	Interactions Focus chain E [auth B] Focus chain G Focus chain I Interactions & Density Focus chain E [auth B] Focus chain G Focus chain I
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain L [auth D] SDF format, chain M [auth D] SDF format, chain N [auth E] SDF format, chain O [auth E] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D] MOL2 format, chain N [auth E] MOL2 format, chain O [auth E] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain L [auth D] mmCIF format, chain M [auth D] mmCIF format, chain N [auth E] mmCIF format, chain O [auth E]	J [auth C] K [auth C] L [auth D] M [auth D] N [auth E] J [auth C], K [auth C], L [auth D], M [auth D], N [auth E], O [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth E] Focus chain O [auth E] Interactions & Density Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth E] Focus chain O [auth E]